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Refactor LEMSSimulation to remove the need of an explicit dict (just use vars(self) instead #427

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merged 2 commits into from
Sep 13, 2024
Merged

Refactor LEMSSimulation to remove the need of an explicit dict (just use vars(self) instead #427

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10e4d09
feat(lemssimulation): replace explicit dict with instance attributes
sanjayankur31 Sep 13, 2024
9a347c8
feat(lems): minor lint fixes
sanjayankur31 Sep 13, 2024
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107 changes: 46 additions & 61 deletions pyneuroml/lems/LEMSSimulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,7 @@
import os
import os.path
import random
import typing
from typing import Optional
from typing import Any, Dict, List, Optional, Union

import airspeed
from neuroml import __version__ as libnml_ver
Expand All @@ -28,20 +27,19 @@ class LEMSSimulation:

TEMPLATE_FILE = "%s/LEMS_TEMPLATE.xml" % (os.path.dirname(__file__))

lems_info: typing.Dict[str, typing.Any] = {}
my_random = random.Random()

def __init__(
self,
sim_id: str,
duration: typing.Union[float, str],
dt: typing.Union[float, str],
target: typing.Optional[str] = None,
duration: Union[float, str],
dt: Union[float, str],
target: Optional[str] = None,
comment: str = "\n\n This LEMS file has been automatically generated using PyNeuroML v%s (libNeuroML v%s)\n\n "
% (pynml_ver, libnml_ver),
lems_file_generate_seed: Optional[typing.Any] = None,
lems_file_generate_seed: Optional[Any] = None,
simulation_seed: int = 12345,
meta: typing.Optional[typing.Dict[str, str]] = None,
meta: Optional[Dict[str, str]] = None,
) -> None:
"""Init a new LEMSSimulation object.

Expand Down Expand Up @@ -105,21 +103,21 @@ def __init__(
else:
dt_mag_ms = float(dt)

self.lems_info["sim_id"] = sim_id
self.lems_info["duration"] = duration_mag_ms
self.lems_info["dt"] = dt_mag_ms
self.lems_info["comment"] = comment
self.lems_info["seed"] = int(simulation_seed)
self.lems_info["report"] = ""
self.sim_id = sim_id
self.duration = duration_mag_ms
self.dt = dt_mag_ms
self.comment = comment
self.seed = int(simulation_seed)
self.report = ""

self.lems_info["include_files"] = []
self.lems_info["displays"] = []
self.lems_info["output_files"] = []
self.lems_info["event_output_files"] = []
self.lems_info["meta"] = meta
self.include_files: List[str] = []
self.displays: List[Dict[str, Any]] = []
self.output_files: List[Dict[str, Any]] = []
self.event_output_files: List[Dict[str, Any]] = []
self.meta = meta

if target:
self.lems_info["target"] = target
self.target = target

if lems_file_generate_seed:
self.my_random.seed(
Expand All @@ -128,22 +126,12 @@ def __init__(
else:
self.my_random.seed(12345)

self.lems_file_name = f"LEMS_{self.lems_info['sim_id']}.xml"
self.lems_file_name = f"LEMS_{self.sim_id}.xml"

def __setattr__(self, attr: typing.Any, value: typing.Any) -> None:
"""Set an attribute value.

:param attr: attribute to set value of
:type attr: Any
:param value: value to set
:type value: Any
:returns: None
:raises AttributeError: if provided attribute is not found in LEMSSimulation.
"""
if attr in self.lems_info.keys():
self.lems_info[attr] = value
else:
raise AttributeError("There is not a field: %s in LEMSSimulation" % attr)
@property
def lems_info(self):
"""Return the attributes"""
return vars(self)

def assign_simulation_target(self, target: str) -> None:
"""Assign a simulation target.
Expand All @@ -152,7 +140,7 @@ def assign_simulation_target(self, target: str) -> None:
:type target: str
:returns: None
"""
self.lems_info["target"] = target
self.target = target

def set_report_file(self, report_file_name: str) -> None:
"""Set a report file.
Expand All @@ -164,7 +152,7 @@ def set_report_file(self, report_file_name: str) -> None:
:returns: None
"""
if report_file_name is not None:
self.lems_info["report"] = ' reportFile="%s"' % report_file_name
self.report = ' reportFile="%s"' % report_file_name

def include_neuroml2_file(
self,
Expand All @@ -190,8 +178,8 @@ def include_neuroml2_file(
full_path = os.path.abspath(relative_to_dir + "/" + nml2_file_name)
base_path = os.path.dirname(full_path)
# logger.info_v("Including in generated LEMS file: %s (%s)"%(nml2_file_name, full_path))
if nml2_file_name not in self.lems_info["include_files"]:
self.lems_info["include_files"].append(nml2_file_name)
if nml2_file_name not in self.include_files:
self.include_files.append(nml2_file_name)

if include_included:
cell = read_neuroml2_file(full_path)
Expand All @@ -212,13 +200,13 @@ def include_lems_file(
:type include_included: bool
:returns: None
"""
if lems_file_name not in self.lems_info["include_files"]:
self.lems_info["include_files"].append(lems_file_name)
if lems_file_name not in self.include_files:
self.include_files.append(lems_file_name)

if include_included:
model = read_lems_file(lems_file_name)
for inc in model.included_files:
self.lems_info["include_files"].append(inc)
self.include_files.append(inc)

def create_display(
self, id: str, title: str, ymin: str, ymax: str, timeScale: str = "1ms"
Expand All @@ -237,8 +225,8 @@ def create_display(
:type timeScale: str
:returns: None
"""
disp = {} # type: dict[str, typing.Any]
self.lems_info["displays"].append(disp)
disp = {} # type: dict[str, Any]
self.displays.append(disp)
disp["id"] = id
disp["title"] = title
disp["ymin"] = ymin
Expand All @@ -259,8 +247,8 @@ def create_output_file(self, id: str, file_name: str):
:type file_name: str
:returns: None
"""
of = {} # type: dict[str, typing.Any]
self.lems_info["output_files"].append(of)
of = {} # type: dict[str, Any]
self.output_files.append(of)
of["id"] = id
of["file_name"] = file_name
of["columns"] = []
Expand All @@ -283,7 +271,7 @@ def create_event_output_file(self, id, file_name, format="ID_TIME"):
:returns: None
"""
eof = {}
self.lems_info["event_output_files"].append(eof)
self.event_output_files.append(eof)
eof["id"] = id
eof["file_name"] = file_name
eof["format"] = format
Expand All @@ -295,7 +283,7 @@ def add_line_to_display(
line_id: str,
quantity: str,
scale: str = "1",
color: typing.Optional[str] = None,
color: Optional[str] = None,
timeScale: str = "1ms",
) -> None:
"""Add a new line to the display
Expand All @@ -316,15 +304,15 @@ def add_line_to_display(
:raises ValueError: if provided `display_id` has not been created yet.
"""
disp = None
for d in self.lems_info["displays"]:
for d in self.displays:
if d["id"] == display_id:
disp = d
if not disp:
raise ValueError(
f"Display with id {display_id} not found. Please check the provided display_id, or create it first."
)

line = {} # type: dict[str, typing.Any]
line = {} # type: dict[str, Any]
disp["lines"].append(line)
line["id"] = line_id
line["quantity"] = quantity
Expand All @@ -348,7 +336,7 @@ def add_column_to_output_file(
:raises ValueError: if provided `output_file_id` has not been created yet.
"""
of = None
for o in self.lems_info["output_files"]:
for o in self.output_files:
if o["id"] == output_file_id:
of = o

Expand All @@ -357,7 +345,7 @@ def add_column_to_output_file(
f"Output file with id {output_file_id} not found. Please check the provided output_file_id, or create it first."
)

column = {} # type: dict[str, typing.Any]
column = {} # type: dict[str, Any]
of["columns"].append(column)
column["id"] = column_id
column["quantity"] = quantity
Expand All @@ -381,15 +369,15 @@ def add_selection_to_event_output_file(
:raises ValueError: if provided `event_output_file_id` has not been created yet.
"""
eof = None
for o in self.lems_info["event_output_files"]:
for o in self.event_output_files:
if o["id"] == event_output_file_id:
eof = o
if not eof:
raise ValueError(
f"Output file with id {event_output_file_id} not found. Please check the provided event_output_file_id, or create it first."
)

selection = {} # type: dict[str, typing.Any]
selection = {} # type: dict[str, Any]
eof["selections"].append(selection)
selection["id"] = event_id
selection["select"] = select
Expand All @@ -406,9 +394,10 @@ def to_xml(self) -> str:
templfile = "." + templfile
with open(templfile) as f:
templ = airspeed.Template(f.read())

return templ.merge(self.lems_info)

def save_to_file(self, file_name: typing.Optional[str] = None):
def save_to_file(self, file_name: Optional[str] = None):
"""Save LEMSSimulation to a file.

:param file_name: name of file to store to.
Expand All @@ -427,18 +416,14 @@ def save_to_file(self, file_name: typing.Optional[str] = None):
self.lems_file_name = file_name

logger.info(
"Writing LEMS Simulation %s to file: %s..."
% (self.lems_info["sim_id"], file_name)
"Writing LEMS Simulation %s to file: %s..." % (self.sim_id, file_name)
)
with open(file_name, "w") as lems_file:
lems_file.write(self.to_xml())
lems_file.flush()
os.fsync(lems_file.fileno())

logger.info(
"Written LEMS Simulation %s to file: %s"
% (self.lems_info["sim_id"], file_name)
)
logger.info("Written LEMS Simulation %s to file: %s" % (self.sim_id, file_name))

return file_name

Expand Down
13 changes: 7 additions & 6 deletions pyneuroml/lems/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,8 @@ def generate_lems_file_for_neuroml(
sim_id: str,
neuroml_file: str,
target: str,
duration: str,
dt: str,
duration: typing.Union[str, float, int],
dt: typing.Union[str, float, int],
lems_file_name: str,
target_dir: str,
nml_doc: typing.Optional[neuroml.NeuroMLDocument] = None,
Expand Down Expand Up @@ -55,9 +55,9 @@ def generate_lems_file_for_neuroml(
:param target: target element
:type target: str
:param duration: simulation duration
:type duration: str
:type duration: str or float or int
:param dt: integration time step
:type dt: str
:type dt: str or float or int
:param lems_file_name: name of LEMS file
:type lems_file_name: str
:param target_dir: directory to place LEMS file in
Expand Down Expand Up @@ -153,7 +153,8 @@ def generate_lems_file_for_neuroml(
else:
nml_doc_inc_not_included = nml_doc

ls.set_report_file(report_file_name)
if report_file_name is not None:
ls.set_report_file(report_file_name)

quantities_saved = []

Expand Down Expand Up @@ -395,7 +396,7 @@ def generate_lems_file_for_neuroml(
for i in range(size):
quantity = quantity_template_e % (population.id, i)
ls.add_selection_to_event_output_file(
eof0, i, quantity, "spike"
eof0, str(i), quantity, "spike"
)
quantities_saved.append(quantity)

Expand Down
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